November 2010

Chimpanzees, our closest living relatives, provide a unique opportunity to study the evolution and adaptations in the human line of rapidly evolving gene families. In this issue of PLoS Genetics, Abi-Rached et al. performed an extensive comparison of the genomics, population biology, and immunology of human and chimpanzee variable receptor–ligand interactions governing Natural Killer cell functions in immune defense and reproduction. These comparisons reveal dramatic qualitative differences between the human and chimpanzee systems, which predominantly derive from adaptations on the human line in response to selective pressures placed on human Natural Killer cells by the competing needs of defense and reproduction.

Image Credit: Emily Wroblewski (Stanford University)

Perspectives

Endless Forms Most Viral

Welkin E. Johnson

PLOS Genetics: published November 18, 2010 | https://doi.org/10.1371/journal.pgen.1001210

Beyond QTL Cloning

Jill T. Anderson, Thomas Mitchell-Olds

PLOS Genetics: published November 11, 2010 | https://doi.org/10.1371/journal.pgen.1001197

Research Articles

Localization of a Guanylyl Cyclase to Chemosensory Cilia Requires the Novel Ciliary MYND Domain Protein DAF-25

Victor L. Jensen, Nathan J. Bialas, Sharon L. Bishop-Hurley, Laurie L. Molday, Katarzyna Kida, Phuong Anh T. Nguyen, Oliver E. Blacque, Robert S. Molday, Michel R. Leroux, Donald L. Riddle

PLOS Genetics: published November 24, 2010 | https://doi.org/10.1371/journal.pgen.1001199

A Novel zf-MYND Protein, CHB-3, Mediates Guanylyl Cyclase Localization to Sensory Cilia and Controls Body Size of Caenorhabditis elegans

Manabi Fujiwara, Takayuki Teramoto, Takeshi Ishihara, Yasumi Ohshima, Steven L. McIntire

PLOS Genetics: published November 24, 2010 | https://doi.org/10.1371/journal.pgen.1001211

Caenorhabditis elegans Cyclin B3 Is Required for Multiple Mitotic Processes Including Alleviation of a Spindle Checkpoint–Dependent Block in Anaphase Chromosome Segregation

Gary M. R. Deyter, Tokiko Furuta, Yasuhiro Kurasawa, Jill M. Schumacher

PLOS Genetics: published November 24, 2010 | https://doi.org/10.1371/journal.pgen.1001218

Leptotene/Zygotene Chromosome Movement Via the SUN/KASH Protein Bridge in Caenorhabditis elegans

Antoine Baudrimont, Alexandra Penkner, Alexander Woglar, Thomas Machacek, Christina Wegrostek, Jiradet Gloggnitzer, Alexandra Fridkin, Franz Klein, Yosef Gruenbaum, Pawel Pasierbek, Verena Jantsch

PLOS Genetics: published November 24, 2010 | https://doi.org/10.1371/journal.pgen.1001219

Systematic Dissection and Trajectory-Scanning Mutagenesis of the Molecular Interface That Ensures Specificity of Two-Component Signaling Pathways

Emily J. Capra, Barrett S. Perchuk, Emma A. Lubin, Orr Ashenberg, Jeffrey M. Skerker, Michael T. Laub

PLOS Genetics: published November 24, 2010 | https://doi.org/10.1371/journal.pgen.1001220

Essential Functions of the Histone Demethylase Lid

Ling Li, Christina Greer, Robert N. Eisenman, Julie Secombe

PLOS Genetics: published November 24, 2010 | https://doi.org/10.1371/journal.pgen.1001221

Nomadic Enhancers: Tissue-Specific cis-Regulatory Elements of yellow Have Divergent Genomic Positions among Drosophila Species

Gizem Kalay, Patricia J. Wittkopp

PLOS Genetics: published November 24, 2010 | https://doi.org/10.1371/journal.pgen.1001222

CTCF-Dependent Chromatin Bias Constitutes Transient Epigenetic Memory of the Mother at the H19-Igf2 Imprinting Control Region in Prospermatogonia

Dong-Hoon Lee, Purnima Singh, Shirley Y. Tsai, Nathan Oates, Alexander Spalla, Claudio Spalla, Lucy Brown, Guillermo Rivas, Garrett Larson, Tibor A. Rauch, Gerd P. Pfeifer, Piroska E. Szabó

PLOS Genetics: published November 24, 2010 | https://doi.org/10.1371/journal.pgen.1001224

Nucleolin Is Required for DNA Methylation State and the Expression of rRNA Gene Variants in Arabidopsis thaliana

Frédéric Pontvianne, Mohamed Abou-Ellail, Julien Douet, Pascale Comella, Isabel Matia, Chinmayi Chandrasekhara, Anne DeBures, Todd Blevins, Richard Cooke, Francisco J. Medina, Sylvette Tourmente, Craig S. Pikaard, Julio Sáez-Vásquez

PLOS Genetics: published November 24, 2010 | https://doi.org/10.1371/journal.pgen.1001225

Endogenous Viral Elements in Animal Genomes

Aris Katzourakis, Robert J. Gifford

PLOS Genetics: published November 18, 2010 | https://doi.org/10.1371/journal.pgen.1001191

Sarcomere Formation Occurs by the Assembly of Multiple Latent Protein Complexes

Yanning Rui, Jianwu Bai, Norbert Perrimon

PLOS Genetics: published November 18, 2010 | https://doi.org/10.1371/journal.pgen.1001208

Mismatch Repair–Independent Increase in Spontaneous Mutagenesis in Yeast Lacking Non-Essential Subunits of DNA Polymerase ε

Anna Aksenova, Kirill Volkov, Jaroslaw Maceluch, Zachary F. Pursell, Igor B. Rogozin, Thomas A. Kunkel, Youri I. Pavlov, Erik Johansson

PLOS Genetics: published November 18, 2010 | https://doi.org/10.1371/journal.pgen.1001209

Altered DNA Methylation in Leukocytes with Trisomy 21

Kristi Kerkel, Nicole Schupf, Kota Hatta, Deborah Pang, Martha Salas, Alexander Kratz, Mark Minden, Vundavalli Murty, Warren B. Zigman, Richard P. Mayeux, Edmund C. Jenkins, Ali Torkamani, Nicholas J. Schork, Wayne Silverman, B. Anne Croy, Benjamin Tycko

PLOS Genetics: published November 18, 2010 | https://doi.org/10.1371/journal.pgen.1001212

Genome-Wide Association Study Identifies Two Novel Regions at 11p15.5-p13 and 1p31 with Major Impact on Acute-Phase Serum Amyloid A

Carola Marzi, Eva Albrecht, Pirro G. Hysi, Vasiliki Lagou, Melanie Waldenberger, Anke Tönjes, Inga Prokopenko, Katharina Heim, Hannah Blackburn, Janina S. Ried, Marcus E. Kleber, Massimo Mangino, Barbara Thorand, Annette Peters, Christopher J. Hammond, Harald Grallert, Bernhard O. Boehm, Peter Kovacs, Ludwig Geistlinger, Holger Prokisch, Bernhard R. Winkelmann, Tim D. Spector, H.-Erich Wichmann, Michael Stumvoll, Nicole Soranzo, Winfried März, Wolfgang Koenig, Thomas Illig, Christian Gieger

PLOS Genetics: published November 18, 2010 | https://doi.org/10.1371/journal.pgen.1001213

The Parental Non-Equivalence of Imprinting Control Regions during Mammalian Development and Evolution

Reiner Schulz, Charlotte Proudhon, Timothy H. Bestor, Kathryn Woodfine, Chyuan-Sheng Lin, Shau-Ping Lin, Marine Prissette, Rebecca J. Oakey, Déborah Bourc'his

PLOS Genetics: published November 18, 2010 | https://doi.org/10.1371/journal.pgen.1001214

RACK-1 Acts with Rac GTPase Signaling and UNC-115/abLIM in Caenorhabditis elegans Axon Pathfinding and Cell Migration

Rafael S. Demarco, Erik A. Lundquist

PLOS Genetics: published November 18, 2010 | https://doi.org/10.1371/journal.pgen.1001215

A Functional Genomics Approach Identifies Candidate Effectors from the Aphid Species Myzus persicae (Green Peach Aphid)

Jorunn I. B. Bos, David Prince, Marco Pitino, Massimo E. Maffei, Joe Win, Saskia A. Hogenhout

PLOS Genetics: published November 18, 2010 | https://doi.org/10.1371/journal.pgen.1001216

Genome-Wide Association Meta-Analysis of Cortical Bone Mineral Density Unravels Allelic Heterogeneity at the RANKL Locus and Potential Pleiotropic Effects on Bone

Lavinia Paternoster, Mattias Lorentzon, Liesbeth Vandenput, Magnus K. Karlsson, Östen Ljunggren, Andreas Kindmark, Dan Mellstrom, John P. Kemp, Caroline E. Jarett, Jeff M. P. Holly, Adrian Sayers, Beate St. Pourcain, Nicholas J. Timpson, Panos Deloukas, George Davey Smith, Susan M. Ring, David M. Evans, Jon H. Tobias, Claes Ohlsson

PLOS Genetics: published November 18, 2010 | https://doi.org/10.1371/journal.pgen.1001217

A Coastal Cline in Sodium Accumulation in Arabidopsis thaliana Is Driven by Natural Variation of the Sodium Transporter AtHKT1;1

Ivan Baxter, Jessica N. Brazelton, Danni Yu, Yu S. Huang, Brett Lahner, Elena Yakubova, Yan Li, Joy Bergelson, Justin O. Borevitz, Magnus Nordborg, Olga Vitek, David E. Salt

PLOS Genetics: published November 11, 2010 | https://doi.org/10.1371/journal.pgen.1001193

An Evolutionary Framework for Association Testing in Resequencing Studies

C. Ryan King, Paul J. Rathouz, Dan L. Nicolae

PLOS Genetics: published November 11, 2010 | https://doi.org/10.1371/journal.pgen.1001202

Epigenetic Silencing of Spermatocyte-Specific and Neuronal Genes by SUMO Modification of the Transcription Factor Sp3

Bastian Stielow, Imme Krüger, Rolf Diezko, Florian Finkernagel, Nynke Gillemans, John Kong-a-San, Sjaak Philipsen, Guntram Suske

PLOS Genetics: published November 11, 2010 | https://doi.org/10.1371/journal.pgen.1001203

Analysis of the 10q11 Cancer Risk Locus Implicates MSMB and NCOA4 in Human Prostate Tumorigenesis

Mark M. Pomerantz, Yashaswi Shrestha, Richard J. Flavin, Meredith M. Regan, Kathryn L. Penney, Lorelei A. Mucci, Meir J. Stampfer, David J. Hunter, Stephen J. Chanock, Eric J. Schafer, Jennifer A. Chan, Josep Tabernero, José Baselga, Andrea L. Richardson, Massimo Loda, William K. Oh, Philip W. Kantoff, William C. Hahn, Matthew L. Freedman

PLOS Genetics: published November 11, 2010 | https://doi.org/10.1371/journal.pgen.1001204

Replication and Recombination Factors Contributing to Recombination-Dependent Bypass of DNA Lesions by Template Switch

Fabio Vanoli, Marco Fumasoni, Barnabas Szakal, Laurent Maloisel, Dana Branzei

PLOS Genetics: published November 11, 2010 | https://doi.org/10.1371/journal.pgen.1001205

A Buoyancy-Based Screen of Drosophila Larvae for Fat-Storage Mutants Reveals a Role for Sir2 in Coupling Fat Storage to Nutrient Availability

Tânia Reis, Marc R. Van Gilst, Iswar K. Hariharan

PLOS Genetics: published November 11, 2010 | https://doi.org/10.1371/journal.pgen.1001206

The Transcriptional Regulator Rok Binds A+T-Rich DNA and Is Involved in Repression of a Mobile Genetic Element in Bacillus subtilis

Wiep Klaas Smits, Alan D. Grossman

PLOS Genetics: published November 11, 2010 | https://doi.org/10.1371/journal.pgen.1001207

Conflict between Noise and Plasticity in Yeast

Ben Lehner

PLOS Genetics: published November 4, 2010 | https://doi.org/10.1371/journal.pgen.1001185

Genetic Basis of Growth Adaptation of Escherichia coli after Deletion of pgi, a Major Metabolic Gene

Pep Charusanti, Tom M. Conrad, Eric M. Knight, Karthik Venkataraman, Nicole L. Fong, Bin Xie, Yuan Gao, Bernhard Ø. Palsson

PLOS Genetics: published November 4, 2010 | https://doi.org/10.1371/journal.pgen.1001186

The Cellular Robustness by Genetic Redundancy in Budding Yeast

Jingjing Li, Zineng Yuan, Zhaolei Zhang

PLOS Genetics: published November 4, 2010 | https://doi.org/10.1371/journal.pgen.1001187

Genome-Wide Effects of Long-Term Divergent Selection

Anna M. Johansson, Mats E. Pettersson, Paul B. Siegel, Örjan Carlborg

PLOS Genetics: published November 4, 2010 | https://doi.org/10.1371/journal.pgen.1001188

Hormad1 Mutation Disrupts Synaptonemal Complex Formation, Recombination, and Chromosome Segregation in Mammalian Meiosis

Yong-Hyun Shin, Youngsok Choi, Serpil Uckac Erdin, Svetlana A. Yatsenko, Malgorzata Kloc, Fang Yang, P. Jeremy Wang, Marvin L. Meistrich, Aleksandar Rajkovic

PLOS Genetics: published November 4, 2010 | https://doi.org/10.1371/journal.pgen.1001190

Human-Specific Evolution and Adaptation Led to Major Qualitative Differences in the Variable Receptors of Human and Chimpanzee Natural Killer Cells

Laurent Abi-Rached, Achim K. Moesta, Raja Rajalingam, Lisbeth A. Guethlein, Peter Parham

PLOS Genetics: published November 4, 2010 | https://doi.org/10.1371/journal.pgen.1001192

ATM Limits Incorrect End Utilization during Non-Homologous End Joining of Multiple Chromosome Breaks

Nicole Bennardo, Jeremy M. Stark

PLOS Genetics: published November 4, 2010 | https://doi.org/10.1371/journal.pgen.1001194

DNA Methylation and Normal Chromosome Behavior in Neurospora Depend on Five Components of a Histone Methyltransferase Complex, DCDC

Zachary A. Lewis, Keyur K. Adhvaryu, Shinji Honda, Anthony L. Shiver, Marijn Knip, Ragna Sack, Eric U. Selker

PLOS Genetics: published November 4, 2010 | https://doi.org/10.1371/journal.pgen.1001196

The Complex Genetic Architecture of the Metabolome

Eva K. F. Chan, Heather C. Rowe, Bjarne G. Hansen, Daniel J. Kliebenstein

PLOS Genetics: published November 4, 2010 | https://doi.org/10.1371/journal.pgen.1001198

The Caenorhabditis elegans Kinesin-3 Motor UNC-104/KIF1A Is Degraded upon Loss of Specific Binding to Cargo

Jitendra Kumar, Bikash C. Choudhary, Raghu Metpally, Qun Zheng, Michael L. Nonet, Sowdhamini Ramanathan, Dieter R. Klopfenstein, Sandhya P. Koushika

PLOS Genetics: published November 4, 2010 | https://doi.org/10.1371/journal.pgen.1001200

The Functional Interplay between Protein Kinase CK2 and CCA1 Transcriptional Activity Is Essential for Clock Temperature Compensation in Arabidopsis

Sergi Portolés, Paloma Más

PLOS Genetics: published November 4, 2010 | https://doi.org/10.1371/journal.pgen.1001201

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Following our own path.

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